Identify DCGs (Differential Coexpressed genes) based on 'Log Ratio Connections'

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Description

A method to pick out DCGs from microarray data based on 'Log Ratio of Connections' (LRC) (Reverter et al. 2006).

Usage

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LRC(exprs.1, exprs.2, link.method = c("qth", "rth", "percent")[1], cutoff)

Arguments

exprs.1

a data frame or matrix for condition A, with rows as variables (genes) and columns as samples.

exprs.2

a data frame or matrix for condition B, with rows as variables (genes) and columns as samples.

link.method

a character string indicating link filtering method, default is 'qth'.

cutoff

cutoff used for link filtration, can be rth, qth, or percent depending on link.method. must be within [0,1].

Details

'Log Ratio of Connections' (LRC) calculates the logarithm of the ratio of the connectivities of a gene between two conditions (Reverter, et al., 2006). A connectivity of zero is changed to one.

Value

LRC

the log Ratio Connections of genes. This measure can be used to rank gene in terms of differential coexpression.

Author(s)

Bao-Hong Liu, Hui Yu, Jing Yang

References

Reverter, A., Ingham, A., Lehnert, S.A., Tan, S.H., Wang, Y., Ratnakumar, A. and Dalrymple, B.P. (2006) Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer, Bioinformatics, 22, 2396-2404.

Examples

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data(exprs)
LRC(exprs[1:100,1:16],exprs[1:100,17:63],link.method = 'qth', cutoff=0.25)